pyjams 2.1

pyjams: a general Python package with a wide variety of miscellaneous utility functions.

A general Python package with a wide variety of miscellaneous utility functions.

About pyjams

pyjams is a general Python package offering a wide variety of miscellaneous functions in different categories, such as reading different file formats, date conversion routines, or calculating Elementary Effects. It has several subpackages offering constants, special functions, or objective functions to be used with scipy.optimize.

The package modernises and makes available routines of the JAMS Python library, which was created 2009 by Matthias Cuntz while at the Department of Computational Hydrosystems, Helmholtz Centre for Environmental Research - UFZ, Leipzig, Germany, and continued while at Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Nancy, France.

The complete documentation of pyjams is available at:

https://mcuntz.github.io/pyjams/

Installation

The easiest way to install is via pip:

pip install pyjams

or via conda:

conda install -c conda-forge pyjams

Requirements

• numpy

• scipy

• matplotlib

• cftime

• netCDF4

• openpyxl

• schwimmbad

Content

Modules and functions are currently provided in the following categories:

• Array Manipulation

• Ascii Files

• Data Processing

• Date and Time

• Grids and Polygons

• Isotopes

• Math

• Meteorology

• Miscellaneous

• Plotting

• Special Files

Functions and modules (alphabetical)

Function/module	Short description
abc2plot	Write a, B, iii), … on a plot
alpha_equ_h2o	Equilibrium fractionation between liquid water and vapour
alpha_kin_h2o	Kinetic fractionation of molecular diffusion of water vapour
argmax	Wrapper for numpy.argmax, numpy.ma.argmax, and max for Python iterables
argmin	Wrapper for numpy.argmin, numpy.ma.argmin, and min for Python iterables
argsort	Wrapper for numpy.argsort, numpy.ma.argsort, and sorted for Python iterables
closest	Index in array which entry is closest to a given number
color	Collection of color palettes and continuous color maps
const	Physical, mathematical, computational, isotope, and material constants
date2date	Convert date representations between different regional variants
date2dec	Return numeric time values given datetime objects or strings, same as date2num
date2en	Convert dates to English date format YYYY-MM-DD hh:mm:ss
date2fr	Convert dates to French date format DD/MM/YYYY hh:mm:ss
date2num	Return numeric time values given datetime objects or strings
date2us	Convert dates to American date format MM/DD/YYYY hh:mm:ss
datetime	Class as cftime.datetime for non-CF-conform calendars
dec2date	Return datetime objects given numeric time values, same as num2date
directories_from_gui	Open dialog to select one directory
directory_from_gui	Open dialog to select several directories
division	Divide two arrays, return ‘otherwise’ if division by 0
div	Divide two arrays, return ‘otherwise’ if division by 0, same as division
eair2mrair	Mixing ratio from partial pressure of water vapour and total pressure
eair2rhair	Relative humidity from partial pressure of water vapour and temperature
eair2shair	Specific humidity from partial pressure of water vapour and total pressure
eair2vpd	Air vapour pressure deficit from partial pressure and temperature
ee	Parameter screening using Morris’ method of Elementary Effects, same as screening
elementary_effects	Morris measures mu, stddev and mu*
en2date	Convert dates to standard date format DD.MM.YYYY hh:mm:ss
en2fr	Convert dates to French date format DD/MM/YYYY hh:mm:ss
en2us	Convert dates to American date format MM/DD/YYYY hh:mm:ss
esat	Saturation vapour pressure over water and ice
file_from_gui	Open dialog to select one file
files_from_gui	Open dialog to select one or several files
fr2date	Convert French dates to standard date format DD.MM.YYYY hh:mm:ss
fr2en	Convert French dates to English date format YYYY-MM-DD hh:mm:ss
fr2us	Convert French dates to American date format MM/DD/YYYY hh:mm:ss
fread	Read numbers from a file into 2D float array
fsread	Read numbers and strings from a file into 2D float and string arrays
functions	Special functions for testing optimisations, sensitivity analysis, several forms of the logistic function and its derivatives, and other functions to be used with scipy.optimize
gridcellarea	Area of grid cells on Earth
infonetcdf	Extract information from netCDF file, same as ncinfo
int2roman	Integer to Roman numeral conversion
kernel_regression	Multi-dimensional non-parametric kernel regression
kernel_regression_h	Determination of bandwidth for kernel regression
mad	Median absolute deviation test
mcPlot	Matthias Cuntz’ standard plotting class
means	Calculate daily, monthly, yearly, etc. means of data
morris_sampling	Sampling of optimised trajectories for Morris measures / Elementary Effects
mrair2eair	Partial pressure of water vapour from mixing ratio and total pressure
ncinfo	Extract information from netCDF file
ncio	netCDF4 functions to copy a netcdf file while doing some transformations on variables and dimensions
ncread	Read variables from netCDF file
num2date	Return datetime objects given numeric time values
pack	Pack array with mask like Fortran intrinsic pack
position	Position arrays of subplots to be used with add_axes
readnetcdf	Read variables from netCDF file, same as ncread
rhair2eair	Partial pressure of water vapour from relative humidity and temperature
rhair2vpd	Air vapour pressure deficit from relative humidity and temperature
roman2int	Roman numeral to integer conversion
sce	Shuffled-Complex-Evolution algorithm for function min(max)imisation
screening	Parameter screening using Morris’ method of Elementary Effects
shair2eair	Partial pressure of water vapour from specific humidity and total pressure
signature2plot	Write a copyright notice on a plot
sread	Read strings from a file into 2D string array
str2tex	Convert strings to LaTeX strings in math environment used by matplotlib’s usetex
tee	Prints arguments on screen and in file, like Unix/Linux tee utility
text2plot	Write text on a plot
unpack	Unpack array using mask like Fortran intrinsic unpack
updatez	Update arrays in uncompressed numpy .npz format
updatez_compressed	Update arrays in compressed numpy .npz format
us2date	Convert dates to standard date format DD.MM.YYYY hh:mm:ss
us2en	Convert dates to English date format YYYY-MM-DD hh:mm:ss
us2fr	Convert dates to French date format DD/MM/YYYY hh:mm:ss
vpd2eair	Partial pressure of water vapour from air vapour pressure deficit and temperature
vpd2rhair	Relative humidity from air vapour pressure deficit and temperature
xlsread	Read numbers and strings from Excel file into 2D float and string arrays, same as xread
xlsxread	Read numbers and strings from Excel file into 2D float and string arrays, same as xread
xread	Read numbers and strings from Excel file into 2D float and string arrays

Functions and modules per category

Array Manipulation

Function/module	Short description
argmax	Wrapper for numpy.argmax, numpy.ma.argmax, and max for Python iterables.
argmin	Wrapper for numpy.argmin, numpy.ma.argmin, and min for Python iterables.
argsort	Wrapper for numpy.argsort, numpy.ma.argsort, and sorted for Python iterables.
closest	Index in array which entry is closest to a given number.
pack	Pack array with mask like Fortran intrinsic pack
unpack	Unpack array using mask like Fortran intrinsic unpack

Ascii Files

Function/module	Short description
fread	Read numbers from a file into 2D float array
fsread	Read numbers and strings from a file into 2D float and string arrays
sread	Read strings from a file into 2D string array

Data Processing

Function/module	Short description
kernel_regression	Multi-dimensional non-parametric kernel regression
kernel_regression_h	Determination of bandwidth for kernel regression
mad	Median absolute deviation test
means	Calculate daily, monthly, yearly, etc. means of data

Date and Time

Function/module	Short description
date2date	Convert date representations between different regional variants
date2dec	Return numeric time values given datetime objects or strings, same as date2num
date2en	Convert dates to English date format YYYY-MM-DD hh:mm:ss
date2fr	Convert dates to French date format DD/MM/YYYY hh:mm:ss
date2num	Return numeric time values given datetime objects or strings
date2us	Convert dates to American date format MM/DD/YYYY hh:mm:ss
datetime	Class as cftime.datetime for non-CF-conform calendars
dec2date	Return datetime objects given numeric time values, same as num2date
en2date	Convert dates to standard date format DD.MM.YYYY hh:mm:ss
en2fr	Convert dates to French date format DD/MM/YYYY hh:mm:ss
en2us	Convert dates to American date format MM/DD/YYYY hh:mm:ss
fr2date	Convert French dates to standard date format DD.MM.YYYY hh:mm:ss
fr2en	Convert French dates to English date format YYYY-MM-DD hh:mm:ss
fr2us	Convert French dates to American date format MM/DD/YYYY hh:mm:ss
num2date	Return datetime objects given numeric time values
us2date	Convert dates to standard date format DD.MM.YYYY hh:mm:ss
us2en	Convert dates to English date format YYYY-MM-DD hh:mm:ss
us2fr	Convert dates to French date format DD/MM/YYYY hh:mm:ss

Grids and Polygons

Function/module	Short description
gridcellarea	Area of grid cells on Earth

Isotopes

Function/module	Short description
alpha_equ_h2o	Equilibrium fractionation between liquid water and vapour
alpha_kin_h2o	Kinetic fractionation of molecular diffusion of water vapour

Math

Function/module	Short description
division	Divide two arrays, return ‘otherwise’ if division by 0
div	Divide two arrays, return ‘otherwise’ if division by 0, same as division
ee	Parameter screening using Morris’ method of Elementary Effects, same as screening
elementary_effects	Morris measures mu, stddev and mu*
functions	Special functions for testing optimisations, sensitivity analysis, several forms of the logistic function and its derivatives, and other functions to be used with scipy.optimize
morris_sampling	Sampling of optimised trajectories for Morris measures / Elementary Effects
sce	Shuffled-Complex-Evolution algorithm for function min(max)imisation
screening	Parameter screening using Morris’ method of Elementary Effects

Meteorology

Function/module	Short description
eair2mrair	Mixing ratio from partial pressure of water vapour and total pressure
eair2rhair	Relative humidity from partial pressure of water vapour and temperature
eair2shair	Specific humidity from partial pressure of water vapour and total pressure
eair2vpd	Air vapour pressure deficit from partial pressure and temperature
esat	Saturation vapour pressure over water and ice
mrair2eair	Partial pressure of water vapour from mixing ratio and total pressure
rhair2eair	Partial pressure of water vapour from relative humidity and temperature
rhair2vpd	Air vapour pressure deficit from relative humidity and temperature
shair2eair	Partial pressure of water vapour from specific humidity and total pressure
vpd2eair	Partial pressure of water vapour from air vapour pressure deficit and temperature
vpd2rhair	Relative humidity from air vapour pressure deficit and temperature

Miscellaneous

Function/module	Short description
const	Physical, mathematical, computational, isotope, and material constants
directories_from_gui	Open dialog to select one directory
directory_from_gui	Open dialog to select several directories
file_from_gui	Open dialog to select one file
files_from_gui	Open dialog to select one or several files
int2roman	Integer to Roman numeral conversion
roman2int	Roman numeral to integer conversion
tee	Prints arguments on screen and in file, like Unix/Linux tee utility

Plotting

Function/module	Short description
abc2plot	Write a, B, iii), … on a plot
color	Collection of color palettes and continuous color maps
int2roman	Integer to Roman numeral conversion
mcPlot	Matthias Cuntz’ standard plotting class
position	Position arrays of subplots to be used with add_axes
roman2int	Roman numeral to integer conversion
signature2plot	Write a copyright notice on a plot
str2tex	Convert strings to LaTeX strings in math environment used by matplotlib’s usetex
text2plot	Write text on a plot

Special Files

Function/module	Short description
infonetcdf	Extract information from netCDF file, same as ncinfo
ncinfo	Extract information from netCDF file
ncio	netCDF4 functions to copy a netcdf file while doing some transformations on variables and dimensions
ncread	Read variables from netCDF file
readnetcdf	Read variables from netCDF file, same as ncread
updatez	Update arrays in uncompressed numpy .npz format
updatez_compressed	Update arrays in compressed numpy .npz format
xlsread	Read numbers and strings from Excel file into 2D float and string arrays, same as xread
xlsxread	Read numbers and strings from Excel file into 2D float and string arrays, same as xread
xread	Read numbers and strings from Excel file into 2D float and string arrays

License

pyjams is distributed under the MIT License. See the LICENSE file for details.

Copyright (c) 2012-2022 Matthias Cuntz, Juliane Mai, Stephan Thober, and Arndt Piayda

The project structure of pyjams has borrowed heavily from welltestpy by Sebastian Müller.